The delay between AUD and SBD is generally about ".001 seconds per foot" from the stacks to the mics, so you will need to trim something off the start of the AUD tracks to align. I generally align by eye and ear, but this is a good approximation. If my mics are 20' from the stacks, the amount that I need to trim off the front of the AUD waveform is about .020 seconds. It might be a bit more... like .025 or so, but it's not .100 or .200.
I generally pick a point in the tracks like a point where it goes from flat line to a spike, figuring out how much I need to chop, then repeat the check at few more points, and kind of do a mental average... using that .001/foot as a sanity check.
I've heard different people say:
a) align for the start of an impulse
b) align for a peak
I've done both, and frequently average between the two.
Most of my mixes are about 50/50 SBD/AUD, unless the SBD is really, really good. In this case I would Amplify both so the peaks hit about -2db. If they both go to 0db, then when they combine to +3db the clipping can become very audible.
This is not an exact science... at least not to me yet.
I use Audacity... it runs on both my Linux and Windows box, and it's free.